SHRIMP 2 SAM output

[ilyagoldin]

I ran gmapper-ls from shrimp 2.0.2, and got this SAM output

HTS2_0006:2:1:985:6502#0/1      16      chr4    97954288        255     11S24M1S        *       0       0       NNNNNNTNNGNCATTTGTAGTTTTCTTTGAATGCTN    ####################################    AS:i:140        H0:i:1  H1:i:2  H2:i:0  NM:i:4  NH:i:11 IH:i:10
HTS2_0006:2:1:985:6502#0/1      0       chr4    30318022        255     2S21M13S        *       0       0       NAGCATTCAAAGAAAACTACAAATGNCNNANNNNNN    ####################################    AS:i:135        H0:i:1  H1:i:2  H2:i:0  NM:i:3  NH:i:11 IH:i:10

How can one QNAME have two different query sequences? Is this because of clipped alignment?

The original (fastaq, now supported by SHRIMP) is

@HTS2_0006:2:1:985:6502#0/1
NAGCATTCAAAGAAAACTACAAATGNCNNANNNNNN
+
####################################

This is the same as the second of the two alignments above, but where did the first come from?

[kmcarr]

The first alignment is to the reverse strand of your reference so it is showing the reverse complement of your query sequence.